Monday, April 24, 2017

65,000 Years Of Beringia In Maps

The linked post shows images of how Beringia looked on a map at regular intervals over the last 65,000 years. The land bridge was more long lived than usually recognized.

Saturday, April 22, 2017

Hobbits Are Not Dwarf H. Erectus

Most people had already rejected the theory that H. florensiensis (Hobbits) were diseased humans. But, this new physical anthropology study rules out the possibility that they are derived from H. erectus, because their bones show more primitive and basal features.

The is notable because it also largely rules out the theory that Hobbits are a subtype of Denisovans or H. heidelbergensis. Instead, it seems likely that they left Africa before or contemporaneously with H. erectus and are closer to H. habilis than any other known species of Homo.
The most comprehensive study on the bones of Homo floresiensis, a species of tiny human discovered on the Indonesian island of Flores in 2003, has found that they most likely evolved from an ancestor in Africa and not from Homo erectus as has been widely believed. The study by The Australian National University (ANU) found Homo floresiensis, dubbed "the hobbits" due to their small stature, were most likely a sister species of Homo habilis -- one of the earliest known species of human found in Africa 1.75 million years ago. 
Data from the study concluded there was no evidence for the popular theory that Homo floresiensis evolved from the much larger Homo erectus, the only other early hominid known to have lived in the region with fossils discovered on the Indonesian mainland of Java. . . .
Homo floresiensis is known to have lived on Flores until as recently as 54,000 years ago.
The study was the result of an Australian Research Council grant in 2010 that enabled the researchers to explore where the newly-found species fits in the human evolutionary tree. 
Where previous research had focused mostly on the skull and lower jaw, this study used 133 data points ranging across the skull, jaws, teeth, arms, legs and shoulders. 
Dr Argue said none of the data supported the theory that Homo floresiensis evolved from Homo erectus. 
"We looked at whether Homo floresiensis could be descended from Homo erectus," she said. 
"We found that if you try and link them on the family tree, you get a very unsupported result. All the tests say it doesn't fit -- it's just not a viable theory." 
Dr Argue said this was supported by the fact that in many features, such as the structure of the jaw, Homo floresiensis was more primitive than Homo erectus. 
"Logically, it would be hard to understand how you could have that regression -- why would the jaw of Homo erectus evolve back to the primitive condition we see in Homo floresiensis?" 
Dr Argue said the analyses could also support the theory that Homo floresiensis could have branched off earlier in the timeline, more than 1.75 million years ago. 
"If this was the case Homo floresiensis would have evolved before the earliest Homo habilis, which would make it very archaic indeed," she said. 
Professor Mike Lee of Flinders University and the South Australian Museum, used statistical modeling to analyse the data. 
"When we did the analysis there was really clear support for the relationship with Homo habilis. Homo floresiensis occupied a very primitive position on the human evolutionary tree," Professor Lee said. 
"We can be 99 per cent sure it's not related to Homo erectus and nearly 100 per cent chance it isn't a malformed Homo sapiens," Professor Lee said.
From Science News.
Although the diminutive Homo floresiensis has been known for a decade, its phylogenetic status remains highly contentious. A broad range of potential explanations for the evolution of this species has been explored. One view is that H. floresiensis is derived from Asian Homo erectus that arrived on Flores and subsequently evolved a smaller body size, perhaps to survive the constrained resources they faced in a new island environment. Fossil remains of H. erectus, well known from Java, have not yet been discovered on Flores. The second hypothesis is that H. floresiensis is directly descended from an early Homo lineage with roots in Africa, such as Homo habilis; the third is that it is Homo sapiens with pathology. 
We use parsimony and Bayesian phylogenetic methods to test these hypotheses. Our phylogenetic data build upon those characters previously presented in support of these hypotheses by broadening the range of traits to include the crania, mandibles, dentition, and postcrania of Homo and Australopithecus. 
The new data and analyses support the hypothesis that H. floresiensis is an early Homo lineage: H. floresiensis is sister either to H. habilis alone or to a clade consisting of at least H. habilis, H. erectus, Homo ergaster, and H. sapiens. A close phylogenetic relationship between H. floresiensis and H. erectus or H. sapiens can be rejected; furthermore, most of the traits separating H. floresiensis from H. sapiens are not readily attributable to pathology (e.g., Down syndrome). The results suggest H. floresiensis is a long-surviving relict of an early (>1.75 Ma) hominin lineage and a hitherto unknown migration out of Africa, and not a recent derivative of either H. erectus or H. sapiens.
Debbie Argue, Colin P. Groves, Michael S.Y. Lee, William L. Jungers. "The affinities of Homo floresiensis based on phylogenetic analyses of cranial, dental, and postcranial characters." Journal of Human Evolution (April 2017).

UPDATE April 24, 2017:
The [Hobbit] skull was astonishingly small: around just 400 cubic centimetres. This was a good 200cc less than the cranial capacity of any fossils then included in our our genus, Homo. Just for comparison, your brain will measure somewhere between 1,000 and 2,000cc. . . . Earlier Homo erectus specimens were known from east and South-East Asia. Perhaps, suggested some researchers, the Flores hominin was an offshoot of Homo erectus, and had undergone “island dwarfing”. Other experts were not so sure; the anatomy of Homo floresiensis seemed too primitive. . . .The shape of the pelvis and the proportions of the limbs looked primitive – reminiscent of australopithecines, or the earliest of human species, Homo habilis, from around 2-3m years ago. But those hominins only ever lived in Africa … as far as we know. . . .

The Flores hominins were, more clearly than ever, rooted deep in that tree: they could not be descendants of Homo erectus. They came from something more primitive – a close cousin of Homo habilis. But what was an ancient-looking hominin like this doing in Indonesia? 
In the most widely accepted model of human evolution today, the first emergence of hominins out of Africa involved Homo erectus, and happened some time after 2m years ago. But Homo floresiensis raises the tantalising possibility of an earlier expansion of hominins – who were probably not-quite-Homo – out of Africa. 
We know, from reconstructions of ancient climate and geography that it certainly would have been possible for hominins to emerge from Africa as far back as 3m years ago. In fact, other large mammal species – including elephants – did just that.
From The Conversation. Another discussion at the same site notes that a different study found a fit with H. Erectus that this study rejects.

The link on the words "climate and geography" above is to the following review article (whose abstract, unfortunately offers more tease than substance).
The past decade has seen the Pliocene and Pleistocene fossil hominin record enriched by the addition of at least ten new taxa, including the Early Pleistocene, small-brained hominins from Dmanisi, Georgia, and the diminutive Late Pleistocene Homo floresiensis from Flores, Indonesia. At the same time, Asia's earliest hominin presence has been extended up to 1.8 Myr ago, hundreds of thousands of years earlier than previously envisaged. Nevertheless, the preferred explanation for the first appearance of hominins outside Africa has remained virtually unchanged. We show here that it is time to develop alternatives to one of palaeoanthropology's most basic paradigms: ‘Out of Africa 1’.
Robin Dennell and Wil Roebroeks, "An Asian perspective on early human dispersal from Africa", 438 Nature 1099-1104 (December 22, 2005).

Meanwhile the brain of H. Naledi is called tiny but advanced.

Friday, April 21, 2017

Oldest Temple In World May Have Been Built In Reaction To A Comet Impact

From the LGM to the Younger Dryas

The Last Glacial Maximum (LGM) was the low point of the last major ice age and took place ca. 18,000 BCE. At that time, most of Europe, Siberia and North America were covered with thick glaciers, human in Europe were confined to three small refugia.

The water used in the glaciers and associated polar ice packs greatly lowered the sea level on Earth, connecting the British Isles and Continental Europe with a land bridge; giving rise to a land bridge across the Bering Strait; connecting many islands in island Southeast Asia to each other and the mainland; connecting Papua New Guinea, Australia and the island of Tasmania; making the water passage to the Andaman Island from mainland Southeast Asia much less daunting; and making it easier to reach Japan from mainland East Asia.

As the Earth warmed up again following the LGM, sea levels rose and the glaciers retreated. This allowed the founding population of the Americas expanded from Beringia into North and South America (ca. 12,000-13,000 BCE), and hunter-gatherers from the European refugia and the Near East repopulated Europe, while those hunter-gatherers and others from Asian refugia repopulated Siberia. Populations in the Americas were isolated from the rest of the world. Island Southeast Asians were isolated from mainland Asia and each other. Papua New Guinea was isolated from Australia. And, the Andaman Islands and Japan became more inaccessible from the mainland. Proto-farming was starting to develop in the Fertile Crescent in the Near East (Mesopotamia, Anatolia and the Levant).

Just as the climate was becoming tolerable for farming in many places, the Younger Dryas event occurred. This was a sudden, global, extreme cooling event that started around 10,800 BCE and lasted about 1400 years. This plunged the world into another severe ice age, although not quite as deep an ice age as the LGM. As noted by an author of a paper discussed last month at this blog:
"[T]he Younger-Dryas coincides with the end of Clovis culture and the extinction of more than 35 species of ice-age animals. Moore says while evidence has shown that some of the animals were on the decline before Younger-Dryas, virtually none are found after it. Moore says that would indicate an extinction event for North America." The animals that went extinct included the mastodon, mammoth and saber-toothed tiger.
So climate change, as well as overhunting, appears to have played an important part in the North American megafauna extinction.

Global deposits of rare elements at the time of the Younger Dryas event similar to those found at the CT boundary created by the comet that destroyed the dinosaurs ca. 65 million years ago have made it increasingly clear that the Younger Dryas event was also caused by an extraterrestrial impact, probably by a comet or asteroid about two-thirds of a mile (one kilometer) in diameter, probably originating in the the Taurid meteor stream given its timing, which has now been established quite precisely.

The place where the Younger Dryas object hit the Earth has not yet been identified. This is in some ways a more difficult task because the impact was smaller, but this difficulty is compensated for, in part, because the Younger Dryas impact was much more recent.

Göbekli Tepe

A National Geographic artists impression of Göbekli Tepe shortly after it was completed.  

The Göbekli Tepe in Southeast Anatolia is a sophisticated stone edifice with carved imagines on it that is arguably the earliest temple or astronomical monument in the world. It is located atop a mountain ridge in the Southeastern Anatolia Region of modern-day Turkey, approximately 12 km (7 mi) northeast of the city of Şanlıurfa, not far north of the middle of the border between Syria and Turkey. The tell has a height of 15 m (49 ft) and is about 300 m (980 ft) in diameter. It is approximately 760 m (2,490 ft) above sea level. It is near the northern peak of the Fertile Crescent.

This is particularly notable because it was built by hunter-gathers before crops or farm animals had been domesticated (although domesticated dogs did exist by that point). Its construction coincides with the Younger Dryas event and it was used for about 2,000 years thereafter (i.e. until about 8,000 BCE) this time period corresponds the the archaeological periods in the Near East known as Pre-pottery Neolithic A (PPNA) and Pre-pottery Neolithic B (PPNB).

A new study suggests that the timing of its construction very close in time to the Younger Dryas event was no coincidence. Instead, Göbekli Tepe was probably the response of this community of hunter-gatherers to the Younger Dryas event. It was an observatory as much as it was a temple.
We have interpreted much of the symbolism of Göbekli Tepe in terms of astronomical events. By matching low-relief carvings on some of the pillars at Göbekli Tepe to star asterisms we find compelling evidence that the famous ‘Vulture Stone’ is a date stamp for 10950 BC ± 250 yrs, which corresponds closely to the proposed Younger Dryas event, estimated at 10890 BC. We also find evidence that a key function of Göbekli Tepe was to observe meteor showers and record cometary encounters
Indeed, the people of Göbekli Tepe appear to have had a special interest in the Taurid meteor stream, the same meteor stream that is proposed as responsible for the Younger-Dryas event. Is Göbekli Tepe the ‘smoking gun’ for the Younger-Dryas cometary encounter, and hence for coherent catastrophism?
Martin B. Sweatman and Dimitrios Tsikritsis, "Decoding Göbekli Tepe with archaeoastronomy: What Does The Fox Say?", 17(1) Mediterranean Archaeology and Archaeometry, 233-250 (2017).

Hat tip to Dienekes' Anthrpology BlogThe title of the paper is a silly allusion to a cult classic cute little pop song with international distribution by international artist Ylvis, who has an interest in archaeological (having also written a song about Stonehenge), whose lyrics discuss the sounds that various kinds of animals make, as well as a reference to one of the carvings at the monument.

Did Bell Beaker People Introduce Modern European Dogs?

Dogs similar to modern European dog breeds start to appear in Europe in about the same time and places as the Bell Beaker people and in at least one instance, accompanying a Bell Beaker man in his burial.

Thursday, April 13, 2017

Blog Post Results In Revision Of Next Edition Of New Trade Non-Fiction Book!

This is so unprecedented that it is newsworthy.

Sometimes, voices in the wilderness are heard, although it helps to have a voice that is timely, frequently amplified through mainstream media sources, and has a particularly knowledgable interlocutor.
April 7, 2017
The Particle Zoo: The Search for the Fundamental Nature of Reality
By Gavin Hesketh
Paperback Edition
Quercus (15 Jun. 2017) 
A few weeks ago, I reviewed Gavin Hesketh’s book The Particle Zoo. I found his introduction to quantum field theory very well done. Considering that he can’t rely on equations, Hesketh gets across a lot of details (notably, what Feynman diagrams do and don’t depict). 
However, I was quite unhappy with various inaccuracies in the book, particularly concerning the search for physics beyond the standard model. 
But then something amazing happened! Hesketh sent me an email a few days ago, saying he read my review and revised the manuscript for the paperback edition to address the criticism. While the changes between the two editions will not be large, it usually doesn’t take more than a sentence or two to add some context or a word of caution. And so, I’m happy to endorse the paperback edition of The Particle Zoo which (according to amazon) will appear on June 15th. 
Posted by Sabine Hossenfelder at 6:37 AM

Wednesday, April 12, 2017

Connecting IceCube To Sesame Street

The high energy events observed at the IceCube Neutrino Observatory have triggered many investigations interpreting the highly energetic neutrinos detected as decay products of heavy unstable Dark Matter particles. However, while very detailed treatments of the IceCube phenomenology exist, only a few references focus on the (non-trivial) Dark Matter production part -- and all of those rely on relatively complicated new models which are not always testable directly. 
We instead investigate two of the most minimal scenarios possible, where the operator responsible for the IceCube events is directly involved in Dark Matter production. We show that the simplest (four-dimensional) operator is not powerful enough to accommodate all constraints. A more non-minimal setting (at mass dimension six), however, can do both fitting all the data and also allowing for a comparatively small parameter space only, parts of which can be in reach of future observations. 
We conclude that minimalistic approaches can be enough to explain all data required, while complicated new physics seems not to be required by IceCube.
Marco Chianese and Alexander Merle, "A Consistent Theory of Decaying Dark Matter Connecting IceCube to the Sesame Street" (April 11, 2017).

Why Sesame Street (emphasis mine)?
The IceCube Neutrino Observatory, a neutrino telescope located at the Amundsen-Scott South Pole Station, is a unique window to observe highly energetic neutrinos reaching the Earth’s surface, originating from sources as close as the upper regions of the atmosphere up to extra-galactic objects. Its applications to closer sources range from a more precise determination of the atmospheric neutrino flux over measuring the properties of active neutrinos and constraining those of sterile neutrinos to astrophysical findings such as the shadowing effect of the moon on cosmic rays. As for the wider sources, IceCube’s goal is to investigate several types of astrophysical neutrino emitters, its possible applications ranging from astrophysical point sources over Dark Matter annihilation to supernovae. Finally, also certain exotic particles may leave visible signatures in the detector, such as magnetic monopoles.

A big surprise in the data taken between 2010 and 2013 was the detections of three very high energy events. These events have been under such scrutiny and have generated such an amount of interest, that they have even been given names after characters of the Sesame Street for better recognition: Ernie (1.14 PeV), Bert (1.04 PeV), and Big Bird (2.2 PeV).
Sociologically, this makes a bit of sense as a lot of researchers publishing papers in this field are at about the age when they have children watching Sesame Street.

Friday, April 7, 2017

Warm Dark Matter Parameter Space

A new paper reviews the remaining parameter space that could be consistent with a warm dark matter model. The range of possible masses and other parameters of these dark matter candidates is quite narrow.

Tuesday, April 4, 2017

Waiting for Ancient DNA Data

The world is waiting for results from three important ancient DNA studies that could address longstanding open questions in historical population genetics, but limited to arguments around the edges using mostly existing information, until then.

* One is a huge dataset of ancient Bell Beaker DNA and related samples that would cast light on the Bell Beaker ancient DNA.

* One is a report on ancient Harappan DNA, the first major ancient DNA result from South Asia. Rumors have purported to leak one of the study's main findings.

* One, which will be longer in coming, is a major Minoan ancient DNA study.

While on their surface these are ancient DNA studies related to archaeological cultures, important historical linguistic issues are related to each. If you know the genetic source of a prehistoric culture, there are fewer uncertainties involved in making inferences about it linguistically.

Further Analysis

One of today's less notable than anticipated pair of papers is closed access, but some interesting points from other papers are found in the comments at Eurogenes' post on them linked above (edited for formatting and punctuation, emphasis mine) provide some interesting commentary on them:

We now know from whole Y chromosome sequencing studies of modern samples that the coalescent time of the most common European sub-clade of R1b-M269 is shallow, 5–7 thousand years (Batini et al. 2015; Hallast et al. 2015; Karmin et al. 2015; Poznik et al. 2016). 
From the aDNA studies we have learned that the oldest R1b-M343 lineages, including 14 KYA Villabruna Man from Italy (Fu et al. 2016) and three European hunter-gatherers and three early farmer samples (Fig. 7), did not belong to the R1b- M269 sub-clade According to the ancient DNA evidence, affinity in their autosomal genes to the early farmers of Atapuerca from Spain (Gunther et . . . 

Late Neolithic, Early Bronze Age and Iron Age samples from Central and Western Europe have typically the R1b-L11, R1a1-Z283 and R1a-M417 (xZ645) affiliation while the samples from the Yamnaya and Samara neighbourhood are different and belong to sub-clades R1b11-Z2105 and R1a2-Z93 (Allentoft et al. 2015; Cassidy et al. 2016; Haak et al. 2015; Mathieson et al. 2015; Schiffels et al. 2016). 
The R1b11-Z2015 lineage is today common in the Caucasus and Volga-Uralic region while being virtually absent in Central and Western Europe (Broushaki et al. 2016). 
Interestingly, the earliest offshoot of extant haplogroup R1b-M343 variation, the V88 subclade, which is currently most common in Fulani speaking populations in Africa (Cruciani et al. 2010) has distant relatives in Early Neolithic samples from across wide geographic area from Iberia, Germany to Samara (Fig. 7). In a similar way, early offshoots of the R1b and R1a phylogenies, including R1b lineages derived at P297 and ancestral at M269, and R1a lineages which are derived at M459.
To digest this, you need a program explaining how the Y-DNA R1a and R1b clades are related to each other.

On the R1a side:

*R1a-M459 (a.k.a. R1a1) is very basal and includes essentially all extant Y-DNA R1a although there are a few intermediate clades with very few representatives between R1a-M420 at the root of R1a and R1a-M459.

* R1a2-Z93 (a.k.a. R1a1a1b2) found mostly in Asia, is a sister clade to R1a1-Z282 (a.k.a. R1a1a1b1a) found mostly in Eastern Europe, and is not ancestral to the Eastern European clade. Both of these are clades within both R1a-M417 (a.k.a. R1a1a1) and R-Z645 (a.k.a. R1a1a1b).

*R1a-M417 (xZ645) (a.k.a. R1a1a1) is the same branch of R1a that includes the Eastern European and Asian clades minus the subclade (R1a1a1b) that includes both of those clades that make up the lion's share of R1a in West Eurasia.

The key point is that the European steppe ancient Y-DNA R1a individuals come are part of an already differentiated Asian clade of R1a (now found mostly in Central Asia and South Asia) which is a sister clade to the European clades rather than being ancestral to them. Likewise outlier pro-Corded Ware ancient Y-DNA R1a in Europe is from a distantly related basal clade of R1a that is not ancestral to the currently predominant clades of Y-DNA R1a found there. 

On the R1b side:

* R1b-M343 (a.k.a. R1b*) is the most basal root of Y-DNA R1b.

* R1b-V88 is a very basal branch of R1b on a different branch than R1b-M269.

* R1b-M269 (a.k.a. R1b1a1a2) is a quite derived branch found mostly in Western Europe.

* R1b-L11 (a.k.a. R-P310/L11* a.ka. R1b1a2a1a1*) is a derived version of R1b-M269 which a paraclade of R1b-L151/P310 that has three sister clades including two common sister clades:R-U106 (a.k.a. R1b1a2a1a1a) found in Germanic Europe, and R-P312 (a.k.a. R1b1a2a1a1b) found in Iberia, British Isles, Italy and France.

* R1b11-Z2105 appears to be a typo or obsolete classification because R1b-Z2105 is actually R1b1a1a2a2, which is the a2 subbranch of R1b-M269, which is a sister clade to R1b-L151/P310. It appears that this may be the same clade or much more closely related to the clade R-Z2103 (a.k.a. R1b1a2a2) which is found in the Balkans and Turkey.

The key point is that the Y-DNA R1b clades found in the ancient DNA of the Yamnaya and Samara are closely related sister clades of those found in Western Europe, rather than being ancestral to them. Likewise, the early outlier instances of ancient Y-DNA R1b in ancient DNA from Europe involves basal sister clades to the predominant R1b-M269 rather than ancestral clades of Y-DNA R1b.

The bottom line is that modern Europeans while related fairly closely to people bearing Y-DNA R1a and R1b on the European steppe identified to date, and in old outlier samples from Europe, and in modern Y-DNA R1b-V88 people mostly in North Africa, are not direct descendants of any of these populations and their clades expanded much more recently and very rapidly.

Another comment states:
Archaeological part (CWC) is actually quite good.
Here is a hint what will BBB show: 
"Bell Beaker groups had by now also emerged on the scene, introducing metallurgy, and they further complicated the mix of cultures and people." 
There are two key-words here - emerged and metallurgy. The first one suggest a rather local development. The second a connection to an originally non-IE way of life, as in this sentence: 
"Extensive exchange systems linked different groups together and secured access to products outside the pastoral economy, such as metal." 
Now we can connect this with the old-new slide about mobility, which also showed that CE BB were less mobile than CWC (you can't be more mobile than shepherds if you're "introducing metallurgy", because metal deposits don't have legs like cows; you can eventually jump from one ore mine to another). 
Another interesting thing is about pottery:

"Corded Ware pottery appeared later in Northern Europe, and we may suggest that this did not happen until women with ceramic skills married into this culture and started to copy wooden, leather and woven containers in clay."

Monday, April 3, 2017

Predicting The Higgs Mass With A Slight SM Extension

A clever new paper makes a slight tweak to GR (a running cosmological constant) and a slight tweak to the Standard Model (adding one massless real scalar boson), and uses it to correctly post-dict the 125 GeV Higgs boson mass, to make the theory fit the cosmology data better, and to solve other theoretical pathologies.

Overall this plan of attack for BSM physics looks promising.

The Long Tail Is Still Making Important Discoveries In Mathematics

AS HE WAS brushing his teeth on the morning of July 17, 2014, Thomas Royen, a little-known retired German statistician, suddenly lit upon the proof of a famous conjecture at the intersection of geometry, probability theory, and statistics that had eluded top experts for decades. 
Known as the Gaussian correlation inequality (GCI), the conjecture originated in the 1950s, was posed in its most elegant form in 1972 and has held mathematicians in its thrall ever since. “I know of people who worked on it for 40 years,” said Donald Richards, a statistician at Pennsylvania State University. “I myself worked on it for 30 years.” 
Royen hadn’t given the Gaussian correlation inequality much thought before the “raw idea” for how to prove it came to him over the bathroom sink. Formerly an employee of a pharmaceutical company, he had moved on to a small technical university in Bingen, Germany, in 1985 in order to have more time to improve the statistical formulas that he and other industry statisticians used to make sense of drug-trial data. In July 2014, still at work on his formulas as a 67-year-old retiree, Royen found that the GCI could be extended into a statement about statistical distributions he had long specialized in. On the morning of the 17th, he saw how to calculate a key derivative for this extended GCI that unlocked the proof. “The evening of this day, my first draft of the proof was written,” he said.
From here.

Sunday, April 2, 2017

Higgs Boson Decays To Tau Leptons Confirm Standard Model

The Standard Model Higgs boson is predicted to sometimes decay to tau leptons (third generation electrons and positrons), at a frequency that is a function of their mass. The Standard Model Higgs boson is also predicted to have no CP violation at leading order.

Both of these predictions hold true experimentally, although neither exclusion of beyond the Standard Model hypotheses is ultra-precise, even though these are the best exclusions available.

The Latest Results

A March 29, 2017 pre-print combining the ATLAS and CMS data from Run-I at the Large Hadron Collider (LHC) on the topic found that the Higgs boson coupling to the tau lepton (which had a 5.5 sigma signal in the combined data) was consistent with the Standard Model prediction to within the limits of experimental error, and that there was no CP violation observed to within the limits of experimental error. The abstract is vacuous, so I'll quote some highlights from the body text instead:
The search for CP violation in the interactions of the newly discovered Higgs boson with the other Standard Model (SM) particles is motivated by the lack of sources of CP violation to explain the baryon asymmetry observed in the Universe. In the SM, no effect of CP violation is expected at LO in the production or decay of the SM Higgs boson. Hence, an observation of CP violation involving the observed Higgs boson would be a strong sign of physics beyond the SM. The H → ττ final state is very powerful for studies of CP invariance of the Higgs boson couplings. It is one of the most sensitive channels for the Vector Boson Fusion (VBF) Higgs boson production and it is the most sensitive for the Higgs boson decay into fermions. With H → ττ events, it is possible to probe the CP structure of both the HVV couplings to gauge bosons in VBF events and also of the H f f couplings to fermions. . . .
In combination with the ATLAS and CMS results in the other Higgs boson decays, these two analyses lead to the observation of the H → ττ decays at 5.5σ and µ = 1.11+0.24 −0.22. From this combination, the signal strengths for the ggF and VBF productions measured in the H → ττ decays are 1.0 +0.6 −0.6 and 1.3 +0.4 −0.4, respectively. . . .
Investigations of CP-violating Higgs boson couplings in the decays into pairs of massive gauge bosons show no deviation from SM. . . .
The observable is a CP-odd Optimal Observable built from the leading-order matrix element for the VBF production. An effective Lagrangian is used to include CP-violating effects from operators with mass dimension up to six in the HVV couplings. The effective Lagrangian assumes that the same coefficient is multiplying the CP-odd structures for the HW+W−, HZZ and Hγγ vertices and that all other couplings are as predicted in the SM. Under these assumptions, the matrix element M is the sum of the SM CP-even contribution MSM and a CP-odd contribution Mcp−odd from the dimension-six operators parametrised by the parameter d˜: 
M = MSM + d˜ · Mcp−odd. 
The Optimal Observable OO is defined as the ratio of the CP-odd interference term between MSM and Mcp−odd to the SM contribution. . . .
Since the Optimal Observable is CP-odd, a non vanishing mean value (OO) not equal to 0 is an indication of CP violation.  
The observed mean values (OO) in the data selected in the signal regions are 0.3 ± 0.5 in the ll channel and −0.3 ± 0.4 in the lh channel. Both results are consistent with zero within uncertainties and show no hints for CP violation. 
Limits on the CP-odd couplings are set based on a combined maximum-likelihood fit to the Optimal Observable distributions in data both in the ll and lh channels. Fig 2 shows the result of this fit for the SM d˜ = 0 hypothesis and the best-fit µ = 1.55+0.87 −0.76 in the lh signal region. The regions d˜ < −0.11 and d˜ > 0.05 are excluded at 68% CL. These intervals are an order of magnitude better than those obtained by ATLAS using the Higgs boson decays into gauge bosons. The analysed data does not provide enough sensitivity to set 95% CL intervals though. 
Bottom Line

The experimentally observed Higgs boson continues to be consistent with the predictions of the Standard Model for the Higgs boson in the face of all experimental tests to date through the completion of Run-I and preliminary partial data from Run-II of the LHC.

Implications For Beyond The Standard Model Physics

Implications Of The Tau Coupling Measurement For BSM Physics

The measurement of the tau coupling is important not just because it shows the Higgs boson is as predicted, but because the properties of the Higgs boson are globally sensitive to the properties of the entire matter content of the Standard Model. This is true because all of the fundamental particles of the Standard Model derive their masses from interactions with the Higgs boson in the Standard Model. 

If there were other fundamental particles that derived their masses from the Higgs boson, the properties of the Higgs boson in its decays that are observed experimentally would be different. The experimental data would be particularly sensitive to any missing heavy fundamental particles, which are the hardest to exclude by other methods. 

For example, if there were another particle that derived its mass from the Higgs boson with a mass greater than the 1.776 GeV of the tau lepton and less than or equal to half of the Higgs boson mass of about 62.5 GeV, this would cause the tau lepton signal strength to be much different than the observed signal. Yet, any deviation from the Standard Model signal strength of more than 59% greater than the Standard Model signal or more than 33% less than the Standard Model signal strength is ruled out with 95% confidence by the Run-I data.

A new heavy particle with a mass between 1.776 GeV and 62.5 GeV would tend to make the tau lepton signal weaker. A new light particle with a mass under 1.776 GeV would tend to make the tau lepton signal stronger. Both these kinds of deviations from the Standard Model are disfavored pretty much to the point of being ruled out, except for a possible new very light particle that derives its mass from Higgs boson interactions, by this measurement.

Of course, none of this is terribly earth shaking news. Any particle interacting with weak force interactions via W boson or Z boson with a mass of under 45 GeV have been ruled out since the LEP experiment operated at the LHC's location before it was dismantled in 2001 to make room for the LHC. And, other data from experiments including Tevatron and the LHC have ruled out new particles in the 45 GeV to 62.5 GeV range long ago.

New particles with masses more than 62.5 GeV that derive their mass from Higgs boson interactions might also impact the Higgs boson signal strength of the tau lepton, but I don't have the expertise to say that with confidence. Apparently percent level deviations in couplings can arise from multi-TeV scale new physics.

Of course, if beyond the Standard Model particles derived their mass entirely via mechanisms that don't involve the Higgs boson, this limitation would no longer apply. The trouble is that most two Higgs doublet models with five Higgs bosons rather than one, or more arcane models with even more Higgs bosons, don't interact with new particles in a manner entirely independent of the Standard Model Higgs boson. So, the tighter the fit of the experimentally observed Higgs boson to the Standard Model Higgs boson is, the less room there is for beyond the Standard Model theories with additional Higgs bosons as well.

What If There Is A New Physics "Desert"?

A scenario in which any beyond the Standard Model high energy physics manifest only at many orders of magnitude above the "electro-weak scale" of a hundreds of GeVs, after a "desert" of new physics, becomes more likely with each passing month as new LHC results are released.

If this is the case, we will probably never be able to observe beyond the Standard Model high energy physics in man-made particle colliders.

Even most "natural experiments" in the vicinity of high energy events related to stars and black holes would not have high enough energies to display beyond the Standard Model physics.

For example, it is a hundred times too cold in the hottest parts of the Sun (about 15,000,000,000 degrees Kelvin, to reach the temperatures where a high energy phenomena predicted by the Standard Model, called quark-gluon plasma, can occur (1 GeV per cubic femtometer, which is equivalent to a temperature of about 2,000,000,000,000 degrees Kelvin), even though this energy level has been reached and this phenomena has been observed, in Earth bound particle accelerators.

The first time humans were able to artificially create these energy densities (a.k.a. temperatures) was in 2015 at the Large Hadron Collider (although non-definitive hints that we might have done it were seen at other colliders as early as 2005). Nothing in the solar system had ever been that hot previously at any time in the four or five billion years since it came into existence. The temperatures reached in Run-II of the LHC on Earth are already hotter than those found in a supernova.

If there is a "desert" before beyond the Standard Model high energy physics, it could easily take temperatures on the order of 200,000,000,000,000,000,000 degrees Kelvin or more to see even a definitive experimental hint of this high energy new physics. There may not be any place in nature in the last 13.5 billion years (i.e. in any directly observable period of time since the Big Bang) that has been that hot. At best, we might find indirect evidence in gravity waves discernible in the cosmic background radiation of the universe that might suggest new physics at those temperatures.

Indeed, if there is a "desert" of beyond the Standard Model high energy physics, the details of these physics would be relevant only philosophically and for cosmology applications, since the vicinity of the Big Bang is the only time those physics would come into play.

Implications Of The Lack Of CP Violation For Cosmology

While the data aren't inconsistent with zero CP violation, the exclusions aren't terribly strong. But, the exclusions are still strong enough, and robust enough since they confirm finding from a different measurement of CP violation by the Higgs boson, to make the Higgs boson a poor candidate to explain the matter-antimatter asymmetry observed in the universe. This key cosmology question, therefore, remains an open one.

The Standard Model has only one source of CP violation (a phase in the CKM matrix) which is small δ13 = 1.20 ± 0.08 radians, when maximal CP violation would be π, commonly approximated as 3.14159 and is insufficient by itself to explain the matter-antimatter asymmetry in the universe. The observed CP violating phase for the W boson interactions of quarks is about 40% of the maximal CP violating phase.

There is almost certainly a second source of CP violation in the Standard Model extended to accommodate neutrino masses (a phase in the PMNS matrix of neutrino oscillation) which is believed to be much larger and near maximal based upon preliminary measurements with large error margins. But, without a bridge that does not exist in the Standard Model between neutrinos, where the CP violation probably occurs, and quarks, where the matter-antimatter asymmetry of the universe is observed, the cosmology problem remains and initial conditions of the universe in which the matter-antimatter asymmetry already exists are necessary.

Weird Polish Trees

I wasn't inspired to do anything for April Fool's Day this year, but here's a stranger than fiction tidbit of reality.

In Poland’s Krzywy Las, or Crooked Forest, the pine trees look like potbellied stick figures. On some 400 trees, the trunks buckle out 90 degrees, creating bark-covered bellies that drag just above the earth, oddly, all pointing in the same direction — north. 
No one knows for certain what caused this unusual stand of trees in a protected forest, just outside the town of Gryfino, Poland. The town was mostly destroyed during World War II, and the truth of the forest was lost with it. . . .
The pine trees, thought to have been planted in the early 1930s, bend at the trunks, and some extend outward around three to nine feet before zipping back up into the air. The trees — around 50 feet high at their tallest — were probably damaged at an early age, causing them to permanently grow this way. But how? . . .
It’s possible that a heavy snowfall covered the trees and continued to weigh them down through spring, when buds sprouted up and grew from the snow-covered trunk. But this wouldn’t explain the straight pines that surround this patch of bent ones.

The prevailing hypothesis is that farmers manipulated the trees in the 1930s to use their bent wood for furniture or ship building, but that the war prevented them from following through.
From the New York Times.

Sunday, March 26, 2017

There Was Intense Selection For Vivax Malaria Protective Genes In Africa 40kya

The Secret History Of Mankind's Struggle With Malaria In Africa

Now, vivax malaria is the second most common variety of malaria discussed in the article below (and is the most common type outside of Africa). According to Wikipedia first discussing malaria generally and then the two most common types of it:
The disease is widespread in the tropical and subtropical regions that exist in a broad band around the equator. This includes much of Sub-Saharan Africa, Asia, and Latin America. In 2015, there were 214 million cases of malaria worldwide resulting in an estimated 438,000 deaths, 90% of which occurred in Africa. . . .  
Although P. falciparum traditionally accounts for the majority of deaths, recent evidence suggests that P. vivax malaria is associated with potentially life-threatening conditions about as often as with a diagnosis of P. falciparum infection.
But, ca. 40,000 years ago in parts of Africa (not those less tropical areas where the Khoi-san bushmen lived), a genetic mutation protective against vivax malaria "conferred a selective advantage of about 4.3%, leading to effective fixation in about 8,000 years." 

A parallel story mostly involving P. falciparum is told in the genetics of similarly intense selective pressure on genes including sickle cell trait, thalassaemia traits, and glucose-6-phosphate dehydrogenase deficiency. The combined lethality of all kinds of malaria was thus almost certainly considerably greater than indicated by the selective advantage against one kind of malaria conferred by this gene (which related to what are called "Duffy antigens") alone.

Duffy antigen genes also have multiple applications in population genetics.

A Hint About Intra-African Human History?

Anatomically modern humans have been present in African from ca. 150,000 to 250,000 years ago and archaic hominins have been present in Africa for millions of years. Moreover, it is unlikely that malaria vivax was limited to modern humans. Many forms of malaria can also affect other great apes beside humans, and archaic hominins would have been very similar to modern humans in terms of traits that would have made them vulnerable to, or resistant to, modern humans.

So, the most notable aspect of the protective Duffy antigen genes in humans is not that they are present, but that they arose so recently and only after the founding population of non-Africans left the continent.

In particular, the TMRCA date for the Duffy antigen gene that has reached fixation in tropical Africans isn't that far from the 60,000 years before present TMRCA date for African Pygmies, an African population with one of the most basal divisions from other modern humans in Africa (together with the Khoisan people who are somewhat more basal) that lives mostly in the rainforests of the vast Congo River basin jungle of tropical Africa.

So, while it could be that modest population sizes meant that it simply took a long time for a protective Duffy antigen mutation to occur, it is also quite plausible that the timing is an indication that modern humans in Africa did not live in tropical areas heavily afflicted with malaria mosquitos until ca. 40,000 years ago (plus however long it took for a mutation to emerge once they started live there).

This, combined with knowledge about which parts of Africa were historically deserts or rain forests could shed a lot of light in the question of the historical range of modern humans and their archaic hominin ancestors in the time frame from their earliest evolution to ca. 40,000 years ago, ruling out much of West Africa and Central Africa from that range.

The Article

As explained by a new article revealing this fact:
The human DARC (Duffy antigen receptor for chemokines) gene encodes a membrane-bound chemokine receptor crucial for the infection of red blood cells by Plasmodium vivax, a major causative agent of malaria. Of the three major allelic classes segregating in human populations, the FY*O allele has been shown to protect against P. vivax infection and is at near fixation in sub-Saharan Africa, while FY*B and FY*A are common in Europe and Asia, respectively. Due to the combination of strong geographic differentiation and association with malaria resistance, DARC is considered a canonical example of positive selection in humans. 
Despite this, details of the timing and mode of selection at DARC remain poorly understood. Here, we use sequencing data from over 1,000 individuals in twenty-one human populations, as well as ancient human genomes, to perform a fine-scale investigation of the evolutionary history of DARC. 
We estimate the time to most recent common ancestor (TMRCA) of the most common FY*O haplotype to be 42 kya (95% CI: 34–49 kya). We infer the FY*O null mutation swept to fixation in Africa from standing variation with very low initial frequency (0.1%) and a selection coefficient of 0.043 (95% CI:0.011–0.18), which is among the strongest estimated in the human genome. We estimate the TMRCA of the FY*A mutation in non-Africans to be 57 kya (95% CI: 48–65 kya) and infer that, prior to the sweep of FY*O, all three alleles were segregating in Africa, as highly diverged populations from Asia and ≠Khomani San hunter-gatherers share the same FY*A haplotypes. We test multiple models of admixture that may account for this observation and reject recent Asian or European admixture as the cause. 
Infectious diseases have undoubtedly played an important role in ancient and modern human history. Yet, there are relatively few regions of the genome involved in resistance to pathogens that show a strong selection signal in current genome-wide searches for this kind of signal. We revisit the evolutionary history of a gene associated with resistance to the most common malaria-causing parasite, Plasmodium vivax, and show that it is one of regions of the human genome that has been under strongest selective pressure in our evolutionary history (selection coefficient: 4.3%). Our results are consistent with a complex evolutionary history of the locus involving selection on a mutation that was at a very low frequency in the ancestral African population (standing variation) and subsequent differentiation between European, Asian and African populations.
Kimberly F. McManus, et al., "Population genetic analysis of the DARC locus (Duffy) reveals adaptation from standing variation associated with malaria resistance in humans" PLOS Genetics (March 10, 2017).


This suggests that vivax malaria was very lethal (or at least reproduction preventing) in tropical Africa at the time, killing 4.3% of the entire unprotected population each generation (and a higher percentage of unprotected people who were infected, as not every single person in each generation would have been infected).

About 6% of the population in malaria vulnerable areas of the world are infected with malaria each year also it is predominantly lethal in children aged five and younger who account for 70% of deaths from malaria. Infection rates are much higher in tropical Africa where about 90% of malaria deaths occur.

Infection rates were much higher, about 15%-30% each year as recently as the early 20th century in Africa and sometimes more; there was a dramatic drop in malaria from 11.4% to 0.4% from 1940 to 1942. It is this pervasive infection rate that makes it particularly deadly. "A 2002 report stated that malaria kills 2.7 million people each year, more than 75 percent of them African children under the age of five. "

Thus, vivax malaria would have been more lethal than

* the Spanish flu of 1918
* untreated whooping cough
* measles in modern developing countries 
* lassa fever
* mumps
* treated Dengue fever
* treated tularemia
* diphtheria
* botulism
* perhaps even untreated typhoid fever or SARS (if the infection rate wasn't that high).

Of course, this lethality estimate assumes that the mutation is 100% protective, which it probably isn't. So, due to its probable less than 100% infection rate and its probable less than 100% protectiveness, the actual lethality of vivax malaria in this time period was probably significantly greater than 4.3% per generation of unprotected people.

Modern malaria (all kinds) kills only about 1 in 300 of people infected with it - this ancient strain that lasted 8,000 years would have been more than 14 times more lethal than malaria is today.

It is also possible that the selective advantage may have had a significant fertility component as opposed to purely a lethality effect since in modern populations: "Malaria in pregnant women is an important cause of stillbirths, infant mortality, abortion [i.e. miscarriage] and low birth weight, particularly in P. falciparum infection, but also with P. vivax." If malaria infection rates were very high (as seems likely), these fertility effects could have given rise to a large share of the selective fitness benefit even if the lethality of an infection was only modest.

New World History - Disease As A Factor In The Slave Trade

This evolutionary history shaped the early days of the Americas by contributing to the history of slavery in the Americas. As a result of genetic adaptations to tropical diseases including vivax malaria, the mortality of African working on plantations in the American South, the Caribbean, and South America was lower than that of Europeans.

This lower mortality rate, in turn, is one of the factors that caused these parts of the America to develop an agricultural economy based upon African slave labor rather than European colonists as the Northern United States and Canada and some other parts of South America did.

Basque Genetics

Duffy antigen genes are one area among many in which Basque population genetics are distinctive (although some assumptions of this 2005 article are now outdated).
The Basques live at the western end of the Pyrenees along the Atlantic Ocean and are thought to represent the descendants of a pre-Neolithic people. They demonstrate marked specificities regarding language and genetics among the European populations. We review the published data on the population genetics and Mendelian disorders of the Basques. 
An atypical distribution in some blood group polymorphisms (ABO, Rhesus, and Duffy) was first found in this population. Subsequently, additional characteristics have been described with regard to proteins (enzymes and immunoglobulins) and the HLA system. The advent of molecular biology methods in the 1990s allowed further insights into Basque population genetics based mainly on Y-chromosome and mitochondrial DNA. In addition, the Basques demonstrate peculiarities regarding the distribution of various inherited diseases (i.e., unusual frequencies or founding effects). Taken together, these data support the idea of an ancient and still relatively unmixed population subjected to genetic drift.
Frederic Bauduer, J. Feingold, and Didier Lacombe, "The Basques: Review of Population Genetics and Mendelian Disorders" 77(5) Human Biology 619-637 (October 2005) (closed access).

Saturday, March 25, 2017

Thursday, March 23, 2017

Mediterranean Farmers Took Local Mesolithic Era Migration Wives

Much of the modern mtDNA of Europe (with exception of mtDNA U and perhaps mtDNA V) is derived from mtDNA clades in West Asia and Southwest Asia. The latest study focused on clades of mtDNA J and mtDNA T in modern Europeans, dating their formative periods via mutation rate dating and phylogeny.

In Central Europe and Iberia, these Near Eastern mtDNA clades arrived with more or less gender balanced first farmer families in the Neolithic revolution. 

But, in central and eastern Mediterranean Europe (presumably Greece, the Balkans, Italy and Southern France), these mtDNA clades arrived in the Mesolithic era, after the Younger Dryas ice age, but before farming was introduced. Local women were then integrated into the farming societies that arrived later in the Mediterranean Neolithic revolution (mostly notably the Cardial Pottery Neolithic).
Important gaps remain in our understanding of the spread of farming into Europe, due partly to apparent contradictions between studies of contemporary genetic variation and ancient DNA. 
It seems clear that farming was introduced into central, northern, and eastern Europe from the south by pioneer colonization. It is often argued that these dispersals originated in the Near East, where the potential source genetic pool resembles that of the early European farmers, but clear ancient DNA evidence from Mediterranean Europe is lacking, and there are suggestions that Mediterranean Europe may have resembled the Near East more than the rest of Europe in the Mesolithic. 
Here, we test this proposal by dating mitogenome founder lineages from the Near East in different regions of Europe. We find that whereas the lineages date mainly to the Neolithic in central Europe and Iberia, they largely date to the Late Glacial period in central/eastern Mediterranean Europe. This supports a scenario in which the genetic pool of Mediterranean Europe was partly a result of Late Glacial expansions from a Near Eastern refuge, and that this formed an important source pool for subsequent Neolithic expansions into the rest of Europe.
Joana B. Pereira. et al., "Reconciling evidence from ancient and contemporary genomes: a major source for the European Neolithic within Mediterranean Europe" Proceedings of the Royal Society B (Biology) (March 22, 2017).

Further discussion of the body text of this paper can be found at Bernard's blog (in French).

The Limits Of Consumer Genomic Ancestry Reports

Razib has a nice discussion of the limitations of ancestry assignment methods in consumer genomic products like 23andMe. He makes a couple of key points:

* South Asia has ten times as much intra-regional variation as Northern Europe, but genomics companies currently make little effort to disaggregate this variation outside Europe.

* Consumer genomic companies are in a bind, because the genomic structure of Europe doesn't track the modern national boundaries well. 

Some of the genomic structure of Europe is more clear at a sub-national region level that may cross national boundaries, and some of it is related to events too deep in prehistory to to well known to the general public (e.g. the hunter-gather, first wave Neolithic, and early Bronze Age population shifts plus some minor or only locally significant matters like admixture arising during European colonial empire periods, and major population disruptions in Austria-Hungary). But, without a lot of context, those distinctions don't make much sense to typical personal genomics company customers.

Still No Evidence Of SUSY

Supersymmetry (i.e. SUSY) is not supported by any experimental evidence that distinguishes it from the Standard Model, and the exclusions are far above the weak scale where it was expected to manifest itself. 
This week results are being presented by the LHC experiments at the Moriond (twitter here) and Aspen conferences. While these so far have not been getting much publicity from CERN or in the media, they are quite significant, as first results from an analysis of the full dataset from the 2015+2016 run at 13 TeV, This is nearly the design energy (14 TeV) and a significant amount of data (36 inverse fb/experiment). The target for this year’s run (physics to start in June) is another 45 inverse fb and we’ll not start to hear about results from that until a year or so from now. For 14 TeV and significantly larger amounts of data, the wait will be until 2021 or so. 
The results on searches for supersymmetry reported this week have all been negative, further pushing up the limits on possible masses of conjectured superparticles. Typical limits on gluino masses are now about 2.0 TeV (see here for the latest), up from about 1.8 TeV last summer (see here). ATLAS results are being posted here, and I believe CMS results will appear here.
From here.

In other news from these conferences in progress, there are no newly announced Higgs boson mass or width results, and the experimentally measured fit of the observed Higgs boson couplings to those predicted by the Standard Model remains very tight (comfortably within one standard deviation of the expected value overall).

No significant BSM physics of any kind has been observed definitively at the LHC, although a handful of moderate significance anomalies have been noted that might or might not amount to anything. None of the anomalies are easy and obvious fits to popular BSM theories akin to SUSY.

Monday, March 20, 2017

Another Introgressing Archaic Hominin Species?

Genetic Evidence of Archaic Introgression

Outside Africa

Somehow I missed a notable conclusion in a paper in Nature Genetics this summer on the genetic origins of the Andamanese people, and a related controversy over it.

This paper shows signs of a non-Neanderthal, non-Denisovan archaic hominin species 1-3% admixture (more if more recently diverged, less if less recently diverged) with a species diverged by about 400,000 years +100,000/-200,000 years from modern humans.[1] While this conclusion has certainly not reached a consensus level based upon this single paper, it is a very notable development. This would mean there were three separate archaic species that introgressed into modern humans outside Africa. The archaic species divergence estimated in the Andamanese study seems too recent to be a Homo Erectuswhich should have diverged ca. 1,900,000 years ago when it left Africa, making Homo erectus too old a source for the archaic admixture that was reportedly observed. Another group of prominent researchers, however, was not able to replicate this result, published a refutation within a week, and thinks that it Andamanese paper is erroneous on this point.[2]

UPDATE March 21, 2017:

An April 30, 2014 pre-print at arXiv that I didn't mention thickens the plot (thanks to Ryan in the comment for pointing it out) reveals contributions from two more archaic hominin species to Eurasian genomes that diverged 859,000 and 3,464,000 years ago, both of which belong to common ancestors of modern humans and Neanderthals.[19] There is no indication, however, that the pre-print was ever published, so it may have gotten bogged down by hurdles or substantially revised over the course of the peer review process. The fact that only one of the many co-authors (Li Jin) has many publications in this area could also explain the lack of publication.


In Africa

In addition there were probably probably one to four archaic species that introgressed into modern humans in Africa but not into modern humans outside Africa.[3][4][5][6] There is also the question of what to make of an extremely old African Y-DNA lineage, A00, which could just be an old modern human or proto-modern human lineage, or could be introgressed from an archaic hominin species.[7]

Matching Genetic Signs Of Introgression To Skeletal Remains

The alleged new introgressing species in South/Southeast Asia and in Africa are statistical ghosts derived from modern human genomes.

Denisovan admixture is associated with only by a few teeth and perhaps a knuckle in addition to a strong genetic signal in a few populations, although possibly a very weak signal in other Asian population.[8][9][10]

Only Neanderthals are represented by ample quantities of bones that have been tested for DNA.[11] Neanderthal introgression was found to have been very recent in an individual from 40,000 years ago in Romania whose ancient DNA was tested.[12] Introgression into Altai Neanderthals from modern humans suggests an introgression event ca. 100,000 years ago, predating the common ancestor of all modern humans outside Africa today and suggesting a two wave migration model for modern humans in which the first wave mostly failed.[13] Some African populations have some Neanderthal admixture due to Eurasian back migration.[14]

UPDATE March 23, 2017:

There were probably at least three distinct waves of Neanderthal admixture, in addition to one wave of Denisovan admixture.[20]


And, while not precisely on point, modern human DNA from an individual who died 40,000 years ago in China has been extracted, which is distinctive East Eurasian rather than West Eurasian, and had modern levels of archaic hominin DNA, suggesting that little or no archaic admixture has taken place in East Asia since then.[15]

We also have bones from Homo floresiensis (a.k.a. hobbits) on the island of Flores, and bones from some archaic looking hominins in China not assigned to a species[16], but similar in brain capacity to modern humans and Neanderthals. We have no genetic information from either, but the former, due to its strategic location at the starting point of high levels of Denisovan DNA, and the latter, due to its evolutionary position and geographic location midway between the Altai and Flores, are both prime candidates for Denisovans.

We also have bones classified as Homo heidelbergensis (a.k.a. Homo rhodesiensis) that lived in Africa, Europe and western Asia between 600,000 and 200,000 years ago," which are both about right in terms of age to be an archaic species admixing with modern humans (somewhere, at least). And, we do have ancient DNA from H. heidelbergensis, which presents a complicated story. The mtDNA looked Denisovan,[17] but the nuclear DNA looked significantly more Neanderthal than Denisovan.[18] This "suggests the Neanderthal-Denisovan split happened before 430,000 years ago" (the date of the specimens from which the samples in Spain were taken). This fits with the notion that H. heidelbergensis is a parent clade to the Neanderthals and that Neanderthals and Denisovans are fairly closely related to each other (compared to modern humans and either Neanderthals or Denisovans). Homo heidelbergensis, or an immediate predecessor in Africa (or perhaps a slightly more remote predecessor like Homo ergaster), could also have been an ancestor (at least partially) of modern humans.

Friday, March 17, 2017

Is Poverty Point, Louisiana Evidence Of Complex Social Organization In Hunter-Gathers?

A short partially animated video by the maker of PhD Comics makes the case that Poverty Point, Louisiana is evidence of a far more sophisticated social organization in hunter-gatherers from 1200 BCE than is commonly assumed. 

Given the surprising short timeline of construction of the largest earth mound there (60-90 days which would have taken 1000 laborers plus supporters), I'm inclined to think that, like the pre-Neolithic temples of the Fertile Crescent like Göbekli Tepe, this may have been a periodic meet-up event of an extended clan of tribes a bit like a modern Olympics or extended family reunion. And, while individual mounds may have been built in one go, the entire cluster of mounds may have been built over the course of multiple generations taking centuries. The Wikipedia account of the Anatolian site below is strikingly similar to the one in the video about Poverty Point:
While the site formally belongs to the earliest Neolithic (PPNA), up to now no traces of domesticated plants or animals have been found. The inhabitants are assumed to have been hunters and gatherers who nevertheless lived in villages for at least part of the year. So far, very little evidence for residential use has been found. Through the radiocarbon method, the end of Layer III can be fixed at about 9000 BCE (see above) but it is believed that the elevated location may have functioned as a spiritual center by 11,000 BCE or even earlier, essentially at the very end of the Pleistocene
The surviving structures, then, not only predate pottery, metallurgy, and the invention of writing or the wheel, they were built before the so-called Neolithic Revolution, i.e., the beginning of agriculture and animal husbandry around 9000 BCE. But the construction of Göbekli Tepe implies organization of an advanced order not hitherto associated with Paleolithic, PPNA, or PPNB societies. 
Archaeologists estimate that up to 500 persons were required to extract the heavy pillars from local quarries and move them 100–500 meters (330–1,640 ft) to the site. The pillars weigh 10–20 metric tons (10–20 long tons; 11–22 short tons), with one still in the quarry weighing 50 tons. It has been suggested that an elite class of religious leaders supervised the work and later controlled whatever ceremonies took place. If so, this would be the oldest known evidence for a priestly caste—much earlier than such social distinctions developed elsewhere in the Near East.
Another possibility, but not really consistent with the lack of evidence of settlement and short time frame of construction locally, at least, would have been a somewhat sedentary lifestyle supported by fishing and proto-farming. But, fishing and proto-farming in the Mississippi Delta era could still have given rise to a larger community population that was relatively localized which would make mobilization of a community to build this monument more feasible. Indeed, it may have even been a Chalcolithic technology civilization. According to articles in Science which I summarized in a 2012 post at this site:
A little more than a thousand years later (flourishing 1600 BCE to 1000 BCE), however, a civilization that appears to be derived from this first wave of mound builders appears at Poverty Point, which is within a day's walk of the earlier sites in Louisiana. This urban center is much larger in scale, perhaps comparable to a medium sized archaic era Greek city state, and shows clear signs of a trade network that extends as far as Milwaukee, Wisconsin in the North and the Ozarks in the West. It used copper and engaged in fine stoneworking. Its trade network may have even extended farther still. The way that its structures are aligned with solstices and equinoxes, its burial practices, its pottery, and the arrangement of structures in the complex, appear to strongly echo and to probably be antecedent to the Mesoamerican civilizations of the Olmecs (from ca. 1200 BCE) . . .
Maize (and hence agriculture) had reached the American Southwest by about 2100 BCE via a highland route from a pre-Olmec civilization in Mexico (see also here). Domesticated pumpkins and gourds were present in Kentucky ca. 3000 BCE, and were independently domesticated in Northeast Mexico and the eastern United States. Given this data, I'm skeptical that Poverty Point was really, as the investigator in the video claims, a hunter-gatherer society. But, there are authoritative investigators of the site who have reached that conclusion.

Maize only reached the Eastern United States around 200 BCE, but the Eastern Agricultural Complex had independently domesticated other plants starting around 1800 BCE. These crops included squash (Cucurbita pepo var. ozarkana), little barley (Hordeum pusillum), goosefoot or lambsquarters (Chenopodium berlandieri), erect knotweed (Polygonum erectum), maygrass (Phalaris caroliniana), sumpweed or marsh elder (Iva annua), and sunflower (Helianthus annuus).
The plants are often divided into "oily" or "starchy" categories. Sunflower and sumpweed have edible seeds rich in oil. Erect knotweed and goosefoot, a leafy vegetable, are starches, as are maygrass and little barley, both of which are grasses that yield grains that may be ground to make flour.
It is plausible to me that non-specialist archaeologists at these sites may not have recognized Eastern Agricultural Complex crops as domesticated plants rather than as wild gathered crops, since most of the EAC crops were later replaced by the maize-bean-squash triad developed in Mexico. 

Also, cooking in stone ovens seems inconsistent with a nomadic hunter-gatherer lifestyle.

It is notable that the construction of the Poverty Point mound is contemporaneous with the climate event that in Europe and the Near East led to a historical phenomena known as Bronze Age collapse. Perhaps the effects of that climate event in the Mississippi Delta area at the time spurred a fresh wave of religious devotion to assuage the gods.

Another reason to have particular interest is Poverty Point is that like Göbekli Tepe, in the Fertile Crescent, this seems to have been the point of genesis of a cultural movement that may be ancestral to a wave of agricultural development and organized civilization that spanned most of one continent and a healthy part of another in both cases. (Links to posts on subsequent possibly related civilizations in North America can be found in this post.)

In the chicken and egg problem of which came first, large scale organized religion, or modern civilization, both of these sites argue in favor of a religion first hypothesis.

LHCb Observes Five New Excited States Of A Known Heavy Baryon

Lubos Motl manages to muse poetic on the observation of five new excited neutral charmed omega baryon resonances at the LHCb experiment. I saw the paper when the pre-print was released earlier this week, and swiftly moved past it with a ho-hum. But, sometimes the most powerful stories are in the telling and not the conclusion, and Motl tells it well. (TD at Quantum Diaries Survivor tells much the same story.)

These particles should exist in the Standard Model and are predicted by QCD. They don't shake any of the known laws of physics.

The results will end up as official data points at the Particle Data Group's catalogue of experimental observations of hadrons (only the ground state and one lighter excited state of neutral charmed omega baryon had been observed until now) which are comparable to the long dull pages of data points in tables in the CRC Handbook of Chemistry and Physics about atoms and molecules. And, this will have value as long as it is easier to put data points in a table based upon experiments than it is to do the calculations from first principles needed to determine those values. (The stories linked to in the latest post at 4Gravitons gives us an inkling of hope that this might not always be the case for evermore, because research that would dramatically simplify QCD calculations if successful is continuing in earnest and making progress.)

The fact that there are five over a 119 MeV mass range is interesting for folks who don't have an intuition about how crowded the hadron mass spectrum is. The narrowness of the peaks in the chart reproduced above, called a "narrow width" means that they decay relatively slowly relative to particles with greater width. (They are still highly unstable, however, lasting only for a tiny fraction of a second.)

The naming conventions for hadrons like these is indeed unnaturally awkward. 

Also, while this is less of a big deal than it was in the early days of particle physics when people thought that all the new particles were fundamental, observing five new resonances for the first time in one experimental run is still better than par for the course in this field. It is certainly worth the self-congratulatory tweet from the lab that brought this to his attention.

UPDATE March 22, 2017: Two new papers make detailed theoretical interpretations of these five resonances: here and here.